Starting phenix.real_space_refine on Wed Jan 22 18:50:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xm7_38466/01_2025/8xm7_38466.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xm7_38466/01_2025/8xm7_38466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xm7_38466/01_2025/8xm7_38466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xm7_38466/01_2025/8xm7_38466.map" model { file = "/net/cci-nas-00/data/ceres_data/8xm7_38466/01_2025/8xm7_38466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xm7_38466/01_2025/8xm7_38466.cif" } resolution = 4.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2049 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 10947 2.51 5 N 2931 2.21 5 O 3206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17190 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5879 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 693} Chain: "B" Number of atoms: 9862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1215, 9862 Classifications: {'peptide': 1215} Link IDs: {'PTRANS': 35, 'TRANS': 1179} Chain: "D" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1416 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 13, 'TRANS': 167} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.71, per 1000 atoms: 0.56 Number of scatterers: 17190 At special positions: 0 Unit cell: (97.09, 174.23, 160.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 3 15.00 Mg 1 11.99 O 3206 8.00 N 2931 7.00 C 10947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 2.4 seconds 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 11 sheets defined 57.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 29 through 41 removed outlier: 3.620A pdb=" N ILE A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.864A pdb=" N ILE A 69 " --> pdb=" O ARG A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 113 through 124 removed outlier: 4.320A pdb=" N GLU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 140 through 167 removed outlier: 4.864A pdb=" N ILE A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.023A pdb=" N GLN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.698A pdb=" N LEU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.555A pdb=" N GLN A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.541A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.908A pdb=" N ASP A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.594A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.676A pdb=" N THR A 447 " --> pdb=" O MET A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 470 Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 514 through 527 Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.672A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.531A pdb=" N ASP A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.654A pdb=" N TYR A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 696 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.879A pdb=" N ASP A 700 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 104 removed outlier: 3.533A pdb=" N VAL B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 removed outlier: 3.817A pdb=" N PHE B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 180 through 206 Processing helix chain 'B' and resid 209 through 219 removed outlier: 4.175A pdb=" N THR B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 409 through 416 Processing helix chain 'B' and resid 521 through 524 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 634 through 642 Processing helix chain 'B' and resid 649 through 658 removed outlier: 4.202A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 667 removed outlier: 3.771A pdb=" N LYS B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 686 through 706 removed outlier: 3.780A pdb=" N ASP B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 711 removed outlier: 5.503A pdb=" N HIS B 711 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 724 removed outlier: 3.888A pdb=" N LYS B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 743 Processing helix chain 'B' and resid 746 through 758 removed outlier: 3.774A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 778 Processing helix chain 'B' and resid 783 through 804 Processing helix chain 'B' and resid 805 through 820 removed outlier: 4.360A pdb=" N ALA B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS B 811 " --> pdb=" O GLU B 807 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 831 removed outlier: 3.927A pdb=" N LEU B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 830 " --> pdb=" O ASP B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 846 Processing helix chain 'B' and resid 852 through 866 removed outlier: 3.774A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 891 Proline residue: B 880 - end of helix removed outlier: 3.576A pdb=" N ASP B 891 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 915 removed outlier: 4.667A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 919 removed outlier: 4.176A pdb=" N GLY B 919 " --> pdb=" O LYS B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 916 through 919' Processing helix chain 'B' and resid 921 through 943 removed outlier: 5.704A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.817A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 970 Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.639A pdb=" N ILE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1033 Processing helix chain 'B' and resid 1034 through 1037 Processing helix chain 'B' and resid 1042 through 1055 removed outlier: 3.591A pdb=" N TYR B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1063 Processing helix chain 'B' and resid 1065 through 1077 removed outlier: 3.822A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 4.153A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1107 through 1114 removed outlier: 4.087A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 Processing helix chain 'B' and resid 1125 through 1140 removed outlier: 3.882A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1162 removed outlier: 3.676A pdb=" N GLU B1150 " --> pdb=" O MET B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1183 Processing helix chain 'B' and resid 1185 through 1212 Processing helix chain 'D' and resid 15 through 25 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.544A pdb=" N TYR D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 164 through 178 removed outlier: 4.007A pdb=" N VAL D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 25 removed outlier: 4.054A pdb=" N TRP A 14 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 12 " --> pdb=" O PRO A 19 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 21 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL A 10 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 23 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A 8 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU A 75 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA A 11 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 77 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 13 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 79 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AA4, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.796A pdb=" N LEU B 38 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ARG B 46 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N MET B 40 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TRP B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 347 removed outlier: 9.566A pdb=" N GLU B 340 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N LEU B 405 " --> pdb=" O GLU B 340 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS B 342 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 403 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 253 Processing sheet with id=AA8, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.825A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.223A pdb=" N TRP B 509 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS B 452 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP B 618 " --> pdb=" O VAL B 571 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 571 " --> pdb=" O ASP B 618 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 497 removed outlier: 7.451A pdb=" N HIS B 533 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA B 546 " --> pdb=" O HIS B 533 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 46 removed outlier: 3.736A pdb=" N ILE D 4 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N VAL D 77 " --> pdb=" O SER D 3 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS D 5 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL D 79 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 7 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS D 81 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 9 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N SER D 83 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LEU D 155 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU D 112 " --> pdb=" O LEU D 155 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4351 1.33 - 1.45: 3260 1.45 - 1.57: 9744 1.57 - 1.69: 5 1.69 - 1.81: 172 Bond restraints: 17532 Sorted by residual: bond pdb=" CG1 ILE B 863 " pdb=" CD1 ILE B 863 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.85e+00 bond pdb=" CB ARG B 931 " pdb=" CG ARG B 931 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.47e+00 bond pdb=" C ILE A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.28e-02 6.10e+03 4.16e+00 bond pdb=" CA ALA B1003 " pdb=" C ALA B1003 " ideal model delta sigma weight residual 1.524 1.479 0.044 2.25e-02 1.98e+03 3.86e+00 bond pdb=" CG GLN B1157 " pdb=" CD GLN B1157 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.03e+00 ... (remaining 17527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 22751 2.28 - 4.57: 817 4.57 - 6.85: 95 6.85 - 9.14: 20 9.14 - 11.42: 5 Bond angle restraints: 23688 Sorted by residual: angle pdb=" N ILE B 204 " pdb=" CA ILE B 204 " pdb=" C ILE B 204 " ideal model delta sigma weight residual 113.53 106.75 6.78 9.80e-01 1.04e+00 4.79e+01 angle pdb=" C LYS A 253 " pdb=" N ALA A 254 " pdb=" CA ALA A 254 " ideal model delta sigma weight residual 120.68 110.18 10.50 1.52e+00 4.33e-01 4.77e+01 angle pdb=" C ARG B 103 " pdb=" N LYS B 104 " pdb=" CA LYS B 104 " ideal model delta sigma weight residual 122.66 113.63 9.03 1.63e+00 3.76e-01 3.07e+01 angle pdb=" C LEU A 228 " pdb=" N ILE A 229 " pdb=" CA ILE A 229 " ideal model delta sigma weight residual 120.24 123.19 -2.95 6.30e-01 2.52e+00 2.20e+01 angle pdb=" C LYS B1184 " pdb=" N TYR B1185 " pdb=" CA TYR B1185 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 ... (remaining 23683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.60: 10423 30.60 - 61.20: 262 61.20 - 91.80: 38 91.80 - 122.40: 2 122.40 - 153.00: 1 Dihedral angle restraints: 10726 sinusoidal: 4475 harmonic: 6251 Sorted by residual: dihedral pdb=" CA VAL D 36 " pdb=" C VAL D 36 " pdb=" N PHE D 37 " pdb=" CA PHE D 37 " ideal model delta harmonic sigma weight residual 180.00 135.90 44.10 0 5.00e+00 4.00e-02 7.78e+01 dihedral pdb=" C4' GTP D 202 " pdb=" C5' GTP D 202 " pdb=" O5' GTP D 202 " pdb=" PA GTP D 202 " ideal model delta sinusoidal sigma weight residual 260.87 107.87 153.00 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" CA ARG B 870 " pdb=" C ARG B 870 " pdb=" N GLN B 871 " pdb=" CA GLN B 871 " ideal model delta harmonic sigma weight residual -180.00 -148.19 -31.81 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 10723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1831 0.050 - 0.101: 660 0.101 - 0.151: 149 0.151 - 0.201: 12 0.201 - 0.251: 6 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CG LEU A 159 " pdb=" CB LEU A 159 " pdb=" CD1 LEU A 159 " pdb=" CD2 LEU A 159 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU B 879 " pdb=" CB LEU B 879 " pdb=" CD1 LEU B 879 " pdb=" CD2 LEU B 879 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PHE B1031 " pdb=" N PHE B1031 " pdb=" C PHE B1031 " pdb=" CB PHE B1031 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2655 not shown) Planarity restraints: 3037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 59 " 0.029 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE B 59 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 59 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 59 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 59 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1043 " 0.018 2.00e-02 2.50e+03 1.73e-02 7.50e+00 pdb=" CG TRP B1043 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B1043 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B1043 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B1043 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1043 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1043 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1043 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1043 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B1043 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 87 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO D 88 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.038 5.00e-02 4.00e+02 ... (remaining 3034 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 439 2.59 - 3.17: 18389 3.17 - 3.74: 31579 3.74 - 4.32: 44210 4.32 - 4.90: 64094 Nonbonded interactions: 158711 Sorted by model distance: nonbonded pdb="MG MG D 201 " pdb=" O2G GTP D 202 " model vdw 2.009 2.170 nonbonded pdb=" O THR B 330 " pdb=" ND1 HIS B 334 " model vdw 2.029 3.120 nonbonded pdb=" O LEU B1120 " pdb=" OG1 THR B1124 " model vdw 2.033 3.040 nonbonded pdb=" O PHE B 843 " pdb=" OG SER B 846 " model vdw 2.036 3.040 nonbonded pdb=" OG SER A 643 " pdb=" OD1 ASN A 653 " model vdw 2.053 3.040 ... (remaining 158706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 39.740 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 17532 Z= 0.432 Angle : 1.013 11.424 23688 Z= 0.577 Chirality : 0.053 0.251 2658 Planarity : 0.006 0.068 3037 Dihedral : 14.707 153.003 6660 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 51.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.17), residues: 2117 helix: -1.65 (0.14), residues: 1051 sheet: -1.88 (0.32), residues: 215 loop : -2.08 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP B1043 HIS 0.014 0.003 HIS A 292 PHE 0.055 0.004 PHE B 59 TYR 0.032 0.003 TYR B 778 ARG 0.012 0.001 ARG B 945 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.2627 (tpt) cc_final: 0.2265 (tpt) REVERT: B 40 MET cc_start: 0.8461 (mmp) cc_final: 0.8256 (mmt) REVERT: B 521 GLU cc_start: 0.9764 (mt-10) cc_final: 0.9531 (mp0) REVERT: B 681 MET cc_start: 0.9454 (mmp) cc_final: 0.9193 (mmm) REVERT: B 764 PHE cc_start: 0.9025 (t80) cc_final: 0.8722 (t80) REVERT: B 1011 MET cc_start: 0.9728 (mmp) cc_final: 0.9453 (mmm) REVERT: B 1090 MET cc_start: 0.9177 (mmp) cc_final: 0.8899 (mmm) REVERT: B 1132 MET cc_start: 0.9432 (tmm) cc_final: 0.9109 (tmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3054 time to fit residues: 49.4389 Evaluate side-chains 88 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 165 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 HIS B 537 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 ASN B1035 GLN ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.069330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.048979 restraints weight = 193126.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.048593 restraints weight = 103667.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.049943 restraints weight = 72795.875| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17532 Z= 0.248 Angle : 0.763 7.815 23688 Z= 0.404 Chirality : 0.047 0.221 2658 Planarity : 0.006 0.114 3037 Dihedral : 8.400 145.257 2300 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.57 % Allowed : 6.30 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2117 helix: -1.07 (0.14), residues: 1128 sheet: -1.76 (0.33), residues: 206 loop : -2.00 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1043 HIS 0.008 0.001 HIS B 154 PHE 0.039 0.002 PHE B 114 TYR 0.028 0.002 TYR B 719 ARG 0.024 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 595 MET cc_start: 0.9186 (mtm) cc_final: 0.8905 (mtt) REVERT: B 681 MET cc_start: 0.9594 (mmp) cc_final: 0.9309 (mmm) REVERT: B 990 PHE cc_start: 0.9335 (m-80) cc_final: 0.8994 (m-80) REVERT: B 1011 MET cc_start: 0.9735 (mmp) cc_final: 0.9373 (mmp) REVERT: B 1090 MET cc_start: 0.9376 (mmp) cc_final: 0.9165 (mmm) REVERT: B 1110 LEU cc_start: 0.9893 (mm) cc_final: 0.9677 (mt) REVERT: B 1131 MET cc_start: 0.9600 (pmm) cc_final: 0.9355 (pmm) REVERT: B 1132 MET cc_start: 0.9453 (tmm) cc_final: 0.9207 (tmm) REVERT: B 1158 GLU cc_start: 0.9304 (tp30) cc_final: 0.8917 (tp30) outliers start: 11 outliers final: 4 residues processed: 126 average time/residue: 0.2914 time to fit residues: 58.6682 Evaluate side-chains 101 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 24 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 174 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS A 633 GLN B 89 GLN B 119 GLN B 213 GLN B 576 ASN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.032323 restraints weight = 195547.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.033248 restraints weight = 138519.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.033964 restraints weight = 107485.360| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 17532 Z= 0.337 Angle : 0.802 14.093 23688 Z= 0.424 Chirality : 0.047 0.272 2658 Planarity : 0.007 0.151 3037 Dihedral : 8.299 146.360 2300 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 34.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.16 % Allowed : 6.82 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.17), residues: 2117 helix: -1.05 (0.14), residues: 1112 sheet: -1.72 (0.33), residues: 201 loop : -1.94 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 41 HIS 0.021 0.002 HIS A 89 PHE 0.036 0.003 PHE D 37 TYR 0.026 0.002 TYR B 719 ARG 0.008 0.001 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 680 MET cc_start: 0.9109 (ppp) cc_final: 0.8846 (ppp) outliers start: 3 outliers final: 1 residues processed: 109 average time/residue: 0.2931 time to fit residues: 51.7241 Evaluate side-chains 92 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 182 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 178 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 376 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.069414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.047943 restraints weight = 191188.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.049346 restraints weight = 94863.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.049704 restraints weight = 57753.502| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17532 Z= 0.223 Angle : 0.726 11.380 23688 Z= 0.379 Chirality : 0.047 0.396 2658 Planarity : 0.006 0.149 3037 Dihedral : 8.066 141.308 2300 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2117 helix: -0.71 (0.14), residues: 1128 sheet: -1.46 (0.35), residues: 188 loop : -1.78 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 41 HIS 0.006 0.001 HIS B 154 PHE 0.034 0.002 PHE D 37 TYR 0.026 0.002 TYR B 719 ARG 0.005 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.2925 (tpt) cc_final: 0.2595 (tpt) REVERT: A 596 GLN cc_start: 0.3720 (OUTLIER) cc_final: 0.3503 (pp30) REVERT: B 681 MET cc_start: 0.9387 (mmm) cc_final: 0.9139 (mmm) REVERT: B 683 MET cc_start: 0.8919 (tmm) cc_final: 0.8553 (tmm) REVERT: B 990 PHE cc_start: 0.9526 (m-10) cc_final: 0.9315 (m-80) REVERT: B 1009 MET cc_start: 0.9577 (ppp) cc_final: 0.9125 (ppp) REVERT: B 1011 MET cc_start: 0.9706 (mmp) cc_final: 0.9355 (mmp) REVERT: B 1090 MET cc_start: 0.9264 (mmp) cc_final: 0.9023 (mmm) REVERT: B 1110 LEU cc_start: 0.9716 (mt) cc_final: 0.9500 (mt) REVERT: B 1158 GLU cc_start: 0.9333 (tp30) cc_final: 0.8952 (tp30) outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 0.3008 time to fit residues: 56.3126 Evaluate side-chains 98 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 51 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 107 optimal weight: 0.3980 chunk 67 optimal weight: 20.0000 chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 53 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.070681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.050074 restraints weight = 191529.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.050562 restraints weight = 104784.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.051467 restraints weight = 61443.491| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17532 Z= 0.192 Angle : 0.705 10.043 23688 Z= 0.364 Chirality : 0.045 0.204 2658 Planarity : 0.006 0.132 3037 Dihedral : 7.790 135.483 2300 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2117 helix: -0.32 (0.15), residues: 1125 sheet: -1.37 (0.35), residues: 194 loop : -1.66 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 14 HIS 0.004 0.001 HIS B 154 PHE 0.036 0.002 PHE B 59 TYR 0.020 0.002 TYR B 719 ARG 0.015 0.001 ARG B1015 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4638 (mmt) cc_final: 0.3921 (ttt) REVERT: B 521 GLU cc_start: 0.9740 (mt-10) cc_final: 0.9500 (mp0) REVERT: B 681 MET cc_start: 0.9493 (mmm) cc_final: 0.9228 (mmm) REVERT: B 683 MET cc_start: 0.9105 (tmm) cc_final: 0.8832 (tmm) REVERT: B 969 TYR cc_start: 0.8264 (m-80) cc_final: 0.8064 (m-80) REVERT: B 990 PHE cc_start: 0.9545 (m-10) cc_final: 0.9317 (m-80) REVERT: B 1009 MET cc_start: 0.9565 (ppp) cc_final: 0.9189 (ppp) REVERT: B 1011 MET cc_start: 0.9615 (mmp) cc_final: 0.9308 (mmp) REVERT: B 1090 MET cc_start: 0.9307 (mmp) cc_final: 0.9051 (mmm) REVERT: B 1158 GLU cc_start: 0.9293 (tp30) cc_final: 0.8882 (tp30) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2810 time to fit residues: 54.4251 Evaluate side-chains 104 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 147 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 207 ASN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 799 ASN ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.068400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.046738 restraints weight = 193036.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.047896 restraints weight = 98168.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.048667 restraints weight = 58605.010| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17532 Z= 0.240 Angle : 0.705 9.663 23688 Z= 0.368 Chirality : 0.045 0.165 2658 Planarity : 0.005 0.124 3037 Dihedral : 7.778 136.776 2300 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2117 helix: -0.27 (0.15), residues: 1128 sheet: -1.15 (0.36), residues: 184 loop : -1.71 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 41 HIS 0.007 0.001 HIS B 154 PHE 0.040 0.002 PHE B 59 TYR 0.020 0.002 TYR B 719 ARG 0.008 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3870 (mmt) cc_final: 0.1844 (ttt) REVERT: A 132 MET cc_start: 0.1379 (tpt) cc_final: 0.0689 (tpt) REVERT: A 154 MET cc_start: 0.2388 (tpt) cc_final: 0.2187 (tpt) REVERT: B 521 GLU cc_start: 0.9735 (mt-10) cc_final: 0.9495 (mp0) REVERT: B 681 MET cc_start: 0.9538 (mmm) cc_final: 0.9228 (mmm) REVERT: B 990 PHE cc_start: 0.9562 (m-10) cc_final: 0.9344 (m-80) REVERT: B 1011 MET cc_start: 0.9682 (mmp) cc_final: 0.9356 (mmp) REVERT: B 1090 MET cc_start: 0.9325 (mmp) cc_final: 0.9064 (mmm) REVERT: B 1158 GLU cc_start: 0.9320 (tp30) cc_final: 0.8936 (tp30) outliers start: 2 outliers final: 1 residues processed: 116 average time/residue: 0.2825 time to fit residues: 53.3587 Evaluate side-chains 100 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 142 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 162 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 59 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.063500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.038951 restraints weight = 197372.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.039738 restraints weight = 151365.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.040354 restraints weight = 124132.684| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17532 Z= 0.200 Angle : 0.697 9.512 23688 Z= 0.361 Chirality : 0.045 0.170 2658 Planarity : 0.005 0.121 3037 Dihedral : 7.715 134.336 2300 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2117 helix: -0.17 (0.15), residues: 1134 sheet: -1.09 (0.37), residues: 183 loop : -1.73 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 41 HIS 0.005 0.001 HIS B 154 PHE 0.031 0.002 PHE B 59 TYR 0.026 0.002 TYR D 72 ARG 0.009 0.001 ARG B 935 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: -0.1512 (tpt) cc_final: -0.1790 (tpt) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.2839 time to fit residues: 52.8777 Evaluate side-chains 97 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 102 optimal weight: 0.0050 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 209 optimal weight: 0.4980 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.069941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.047862 restraints weight = 190024.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.049404 restraints weight = 92407.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.050199 restraints weight = 55564.887| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17532 Z= 0.191 Angle : 0.694 9.105 23688 Z= 0.361 Chirality : 0.045 0.185 2658 Planarity : 0.005 0.115 3037 Dihedral : 7.658 132.167 2300 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.05 % Allowed : 1.72 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2117 helix: -0.09 (0.15), residues: 1137 sheet: -1.16 (0.36), residues: 198 loop : -1.63 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 41 HIS 0.004 0.001 HIS B 154 PHE 0.031 0.002 PHE B 59 TYR 0.020 0.002 TYR B 969 ARG 0.006 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.1500 (tpt) cc_final: 0.1112 (tpt) REVERT: A 602 ASP cc_start: 0.8542 (p0) cc_final: 0.8161 (t0) REVERT: B 470 MET cc_start: 0.8814 (pmm) cc_final: 0.8460 (pmm) REVERT: B 529 PHE cc_start: 0.9354 (m-10) cc_final: 0.8910 (m-80) REVERT: B 681 MET cc_start: 0.9304 (mmm) cc_final: 0.9071 (mmm) REVERT: B 990 PHE cc_start: 0.9258 (m-10) cc_final: 0.8912 (m-80) REVERT: B 1009 MET cc_start: 0.9508 (ppp) cc_final: 0.9128 (ppp) REVERT: B 1011 MET cc_start: 0.9655 (mmp) cc_final: 0.9301 (mmp) REVERT: B 1090 MET cc_start: 0.9270 (mmp) cc_final: 0.8933 (mmm) REVERT: B 1110 LEU cc_start: 0.9749 (mt) cc_final: 0.9538 (mt) REVERT: B 1158 GLU cc_start: 0.9324 (tp30) cc_final: 0.8969 (tp30) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.2790 time to fit residues: 53.8207 Evaluate side-chains 100 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 123 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 163 optimal weight: 0.0980 chunk 192 optimal weight: 7.9990 chunk 158 optimal weight: 0.0000 chunk 188 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.068814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.047079 restraints weight = 192592.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.048151 restraints weight = 99657.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.049018 restraints weight = 60646.039| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17532 Z= 0.216 Angle : 0.707 9.212 23688 Z= 0.366 Chirality : 0.045 0.178 2658 Planarity : 0.005 0.112 3037 Dihedral : 7.680 132.680 2300 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.05 % Allowed : 0.83 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2117 helix: -0.12 (0.15), residues: 1139 sheet: -1.12 (0.37), residues: 191 loop : -1.65 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 41 HIS 0.005 0.001 HIS B 567 PHE 0.028 0.002 PHE B 59 TYR 0.026 0.002 TYR B 969 ARG 0.012 0.001 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.1400 (tpt) cc_final: 0.1149 (tpt) REVERT: A 309 MET cc_start: 0.2317 (tpt) cc_final: 0.2094 (tpt) REVERT: A 481 MET cc_start: 0.4832 (mmp) cc_final: 0.4460 (mtp) REVERT: A 602 ASP cc_start: 0.8545 (p0) cc_final: 0.8138 (t0) REVERT: B 470 MET cc_start: 0.8766 (pmm) cc_final: 0.8425 (pmm) REVERT: B 529 PHE cc_start: 0.9331 (m-10) cc_final: 0.8862 (m-80) REVERT: B 595 MET cc_start: 0.9095 (mtm) cc_final: 0.8893 (mpp) REVERT: B 990 PHE cc_start: 0.9320 (m-10) cc_final: 0.8988 (m-80) REVERT: B 1009 MET cc_start: 0.9495 (ppp) cc_final: 0.9112 (ppp) REVERT: B 1011 MET cc_start: 0.9691 (mmp) cc_final: 0.9349 (mmp) REVERT: B 1090 MET cc_start: 0.9283 (mmp) cc_final: 0.8989 (mmm) REVERT: B 1110 LEU cc_start: 0.9740 (mt) cc_final: 0.9525 (mt) REVERT: B 1158 GLU cc_start: 0.9334 (tp30) cc_final: 0.9019 (tp30) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.2810 time to fit residues: 52.6812 Evaluate side-chains 100 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 17 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 171 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 HIS ** B1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.057844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.029267 restraints weight = 183644.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.029856 restraints weight = 134442.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.030418 restraints weight = 107419.239| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17532 Z= 0.346 Angle : 0.824 13.005 23688 Z= 0.434 Chirality : 0.049 0.182 2658 Planarity : 0.006 0.108 3037 Dihedral : 8.052 138.332 2300 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 2117 helix: -0.61 (0.14), residues: 1149 sheet: -1.00 (0.39), residues: 178 loop : -1.85 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1043 HIS 0.007 0.002 HIS B 154 PHE 0.034 0.003 PHE B 59 TYR 0.025 0.003 TYR B 969 ARG 0.007 0.001 ARG A 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: -0.2221 (tpt) cc_final: -0.2510 (tpt) REVERT: A 154 MET cc_start: 0.3465 (tpt) cc_final: 0.3211 (tpt) REVERT: A 481 MET cc_start: 0.2796 (mmp) cc_final: 0.2450 (mtp) REVERT: B 680 MET cc_start: 0.9069 (ppp) cc_final: 0.8603 (ppp) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2746 time to fit residues: 49.5762 Evaluate side-chains 92 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 53 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 0.0020 chunk 182 optimal weight: 0.0470 chunk 38 optimal weight: 30.0000 chunk 85 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 overall best weight: 1.1688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 537 GLN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.062572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.039231 restraints weight = 196118.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.040235 restraints weight = 140961.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.040964 restraints weight = 110357.568| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 17532 Z= 0.198 Angle : 0.733 10.385 23688 Z= 0.377 Chirality : 0.047 0.624 2658 Planarity : 0.005 0.113 3037 Dihedral : 7.805 134.986 2300 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.18), residues: 2117 helix: -0.19 (0.15), residues: 1139 sheet: -1.17 (0.37), residues: 202 loop : -1.62 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 41 HIS 0.006 0.001 HIS B 924 PHE 0.024 0.002 PHE B 59 TYR 0.025 0.002 TYR B 969 ARG 0.007 0.001 ARG A 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5471.45 seconds wall clock time: 99 minutes 49.68 seconds (5989.68 seconds total)